#!/bin/bash

# This wrapper is for Genemark 4.371 on Expanse.

export MODULEPATH=/expanse/projects/ngbt/opt/expanse/modules:$MODULEPATH

start=$(date +%s)
/expanse/projects/ngbt/opt/expanse/braker/GeneMark/gmes_linux_64_4/gmes_petap.pl $*
end=$(date +%s)
elapsed=$((end-start))
echo Elapsed time = $elapsed s

for f in *; do
    if [[ -d $f ]]; then
        jar cvf ${f}.zip $f
        echo "archived subdir $f as ${f}.zip"
    fi
done
echo "... moving on"